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1 Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
2 Department of Food and Life Science, Sungkyunkwan University, Chunchun-dong 300, Jangan-gu, Suwon, Korea
3 National Research Laboratory of Molecular Ecosystematics, Institute of Probionic, Probionic Corporation, Bio-venture Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
Correspondence
Yong-Ha Park
yhpark{at}kribb.re.kr
| ABSTRACT |
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The GenBank accession numbers for the 16S rDNA sequences of strains TF-11T and TF-12T are AF483624 and AF483625.
An extended phylogenetic tree is available as supplementary material in IJSEM Online.
| INTRODUCTION |
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| METHODS |
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Morphological and physiological characterization.
Cell morphology was examined by light microscopy and TEM. Flagellum type was examined by TEM using cells from exponentially growing cultures. The cells were negatively stained with 1 % (w/v) phosphotungstic acid and, after air drying, the grids were examined using a model CM-20 TEM (Philips). The Gram reaction was determined using the bioMérieux Gram stain kit according to the manufacturer's instructions. Catalase activity was determined by bubble production in a 3 % (v/v) hydrogen peroxide solution. Oxidase activity was determined by oxidation of 1 % p-aminodimethylaniline oxalate. Urease activity was determined as described by Cowan & Steel (1965)
, carried out in the presence and absence of 3 % (w/v) NaCl. Hydrolysis of casein and starch was determined as described by Cowan & Steel (1965)
. Hydrolysis of gelatin was determined as described by Cowan & Steel (1965)
, in the presence and absence of 3 % (w/v) NaCl. Hydrolysis of aesculin and Tween 80 was determined as described by Cowan & Steel (1965)
or performed on MA with the concentration of substrates described previously (Cowan & Steel, 1965
). Nitrate reduction was determined as described by Lanyi (1987)
, in the presence and absence of 3 % (w/v) NaCl. Hydrolysis of hypoxanthine, tyrosine and xanthine was examined on MA with substrate concentrations described previously (Cowan & Steel, 1965
). Acid production from carbohydrates was determined as described by Leifson (1963)
and using the API 50CH system (bioMérieux). Cell mass of strains TF-11T and TF-12T was suspended in 2 ml artificial sea water which contained (l-1 distilled water) 23·6 g NaCl, 0·64 g KCl, 4·53 g MgCl2.6H2O, 5·94 g MgSO4.7H2O and 1·3 g CaCl2.2H2O (Levring, 1946
). This suspension was added to API 50CHB medium. Growth under anaerobic conditions was determined after incubation in an anaerobic chamber with MA that had been prepared anaerobically. Growth at various NaCl concentrations was investigated on MA or in MB. Growth at various temperatures was measured on MA at 455 °C.
Isolation of DNA.
Chromosomal DNA was isolated and purified according to Yoon et al. (1996)
, with the exception that ribonuclease T1 was used together with ribonuclease A.
Chemotaxonomic characterization.
The isomer type of diamino acid of the cell-wall peptidoglycan was determined by the method of Komagata & Suzuki (1987)
. Menaquinones were analysed as described previously (Komagata & Suzuki, 1987
) using reversed-phase HPLC. For quantitative analysis of cellular fatty acid compositions, a loop of cell mass was harvested and fatty acid methyl esters were prepared and identified following the instructions of the Microbial Identification system (MIDI).
Determination of G+C content.
The G+C content was determined by the method of Tamaoka & Komagata (1984)
. DNA was hydrolysed and the resultant nucleotides were analysed by reversed-phase HPLC.
DNADNA hybridization.
DNADNA hybridization was performed fluorometrically by the method of Ezaki et al. (1989)
using photobiotin-labelled DNA probes and microdilution wells. Hybridization was performed with five replications for each sample. Of the values obtained, the highest and lowest values in each sample were excluded. DNADNA relatedness values are expressed as the mean of the remaining three values.
16S rDNA sequencing and phylogenetic analysis.
16S rDNA was amplified by PCR using two universal primers as described previously (Yoon et al., 1998
). The PCR product was purified with a QIAquick PCR purification kit (Qiagen). Sequencing of the purified 16S rDNA was performed using an ABI PRISM BigDye Terminator cycle sequencing ready reaction kit (Applied Biosystems) as recommended by the manufacturer. The purified sequencing reaction mixtures were electrophoresed automatically using an Applied Biosystems model 377 automatic DNA sequencer. Alignment of sequences was carried out using CLUSTAL W software (Thompson et al., 1994
). Gaps at the 5' and 3' ends of the alignment were omitted from further analysis. Phylogenetic trees were inferred using three tree-making algorithms, the neighbour-joining (Saitou & Nei, 1987
), maximum-likelihood (Felsenstein, 1981
) and maximum-parsimony (Kluge & Farris, 1969
) methods contained within the PHYLIP package (Felsenstein, 1993
). Evolutionary distance matrices for the neighbour-joining method were calculated using the algorithm of Jukes & Cantor (1969)
with the program DNADIST. The stability of relationships was assessed by a bootstrap analysis based on 1000 resampling of the neighbour-joining dataset using the programs SEQBOOT, DNADIST, NEIGHBOR and CONSENSE of the PHYLIP package.
| RESULTS AND DISCUSSION |
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Conclusions
16S rDNA sequence comparison showed that strains TF-11T and TF-12T exhibited closest phylogenetic affinities to Bacillus species. Phylogenetic analysis based on 16S rDNA sequences shows that the two strains form distinct phylogenetic lineages within the evolutionary radiation enclosed by the genus Bacillus (Fig. 2
). The results obtained in the morphological and chemotaxonomic analyses are consistent with the results of 16S rDNA sequence comparison and phylogenetic inference (Table 1
). Strains TF-11T and TF-12T could be clearly differentiated from each other in their morphological and physiological characteristics. There are distinct morphological differences between them, including colony colour, flagellum type and endospore position. There are also some physiological differences between strains TF-11T and TF-12T, such as tolerance of NaCl, temperature and pH for growth, their ability to hydrolyse some substrates and acid production from carbohydrates (Table 1
). It is noteworthy that strains TF-11T and TF-12T show distinct differences in G+C content and in proportions of some fatty acids, particularly iso- and anteiso-C15 : 0 (Table 2
). The mean level of DNADNA relatedness between the two strains is approximately 7 %. This genomic relatedness provides decisive evidence that strains TF-11T and TF-12T are members of different genomic species (Wayne et al., 1987
). The 16S rDNA sequence similarity values of strains TF-11T and TF-12T to the type strains of other Bacillus species are respectively less than 96·0 and 96·3 %. There are widely accepted criteria for delineating species in current bacteriology, stating that strains with a level of DNA relatedness of less than 70 % or with more than 3 % difference in 16S rDNA sequences are considered to represent different species (Wayne et al., 1987
; Stackebrandt & Goebel, 1994
). Sequence similarity values obtained for strains TF-11T and TF-12T and the type strains of all Bacillus species with validly published names are low enough to categorize strains TF-11T and TF-12T as two distinct species within the genus Bacillus. On the basis of the data described above, strains TF-11T and TF-12T should be placed in the genus Bacillus as two distinct novel species, for which the names Bacillus marisflavi sp. nov. and Bacillus aquimaris sp. nov., respectively, are proposed.
Description of Bacillus marisflavi sp. nov.
Bacillus marisflavi (ma.ris.fla'vi. L. gen. neut. n. maris of the sea; L. masc. adj. flavus yellow; N.L. gen. masc. n. marisflavi of the Yellow Sea).
Cells are aerobic rods, 0·60·8x1·53·5 µm. Gram-positive, but Gram-variable in older cultures. Motile by means of a single polar flagellum. Central or subterminal ellipsoidal endospores are observed in swollen sporangia. Colonies are smooth, circular to slightly irregular, slightly raised, pale yellow in colour and 24 mm in diameter after 3 days at 30 °C on MA. Optimal growth temperature is 3037 °C. Growth occurs at 10 and 47 °C, but not at 4 or above 48 °C. Optimal growth pH is 6·08·0. Growth is observed at pH 4·5, but not at pH 4·0. Optimal growth occurs in the presence of 25 % (w/v) NaCl. Growth occurs in the presence of 016 % (w/v) NaCl. Growth does not occur under anaerobic conditions on MA. Catalase-positive. Oxidase- and urease-negative. Aesculin and casein are hydrolysed. Hypoxanthine, starch, Tween 80, tyrosine and xanthine are not hydrolysed. Acid is produced from D-cellobiose, D-fructose, D-glucose, maltose, D-mannitol, D-mannose, melibiose, D-ribose, stachyose, sucrose, D-trehalose and D-xylose and produced weakly from D-galactose and D-raffinose. Acid is not produced from adonitol, L-arabinose, lactose, D-melezitose, myo-inositol, L-rhamnose or D-sorbitol. Results using the API 50CHB system show that acid is produced from aesculin, arbutin, gentiobiose, glycerol, methyl
-D-mannoside and salicin, but not from N-acetylglucosamine, amygdalin, D-arabinose, D-arabitol, L-arabitol, dulcitol, erythritol, D-fucose, L-fucose, gluconate, glycogen, inulin, 2-ketogluconate, 5-ketogluconate, D-lyxose, methyl
-D-glucoside, methyl
-D-xylose, sorbose, starch, D-tagatose, D-turanose, xylitol or L-xylose. The cell-wall peptidoglycan contains meso-diaminopimelic acid. The predominant menaquinone is MK-7. The major fatty acids are anteiso-C15 : 0 and iso-C15 : 0. The G+C content of the type strain is 49 mol% (determined by HPLC).
The type strain, TF-11T (=KCCM 41588T=JCM 11544T), was isolated from sea water of a tidal flat of the Yellow Sea in Korea.
Description of Bacillus aquimaris sp. nov.
Bacillus aquimaris (a.qui.ma'ris. L. n. aqua water; L. gen. n. maris of the sea; N.L. gen. n. aquimaris of the water of the sea).
Cells are aerobic rods, 0·50·7x1·23·5 µm. Gram-variable. Motile by means of peritrichous flagella. Central ellipsoidal endospores are observed in large, swollen sporangia. Colonies are circular to slightly irregular, slightly raised, pale orange-yellow in colour and 24 mm in diameter after 3 days at 30 °C on MA. Optimal growth temperature is 3037 °C. Growth occurs at 10 and 44 °C, but not at 4 or above 45 °C. Optimal growth pH is 6·07·0; no growth is observed at pH 9·0 or 4·5. Optimal growth occurs in the presence of 25 % (w/v) NaCl. Growth is poor in the absence of NaCl, but occurs in the presence of up to 18 % (w/v) NaCl. Growth does not occur under anaerobic conditions on MA. Catalase-positive. Oxidase- and urease-negative. Casein, starch and Tween 80 are hydrolysed. Aesculin, hypoxanthine, tyrosine and xanthine are not hydrolysed. Acid is produced from D-fructose, D-glucose, maltose, D-ribose, sucrose and D-trehalose. Acid is not produced from adonitol, L-arabinose, D-cellobiose, D-galactose, lactose, D-mannitol, D-mannose, D-melezitose, melibiose, myo-inositol, D-raffinose, L-rhamnose, D-sorbitol, stachyose or D-xylose. Results using the API 50CHB system show that acid is produced from glycogen, 5-ketogluconate and starch, but not from N-acetylglucosamine, aesculin, amygdalin, D-arabinose, D-arabitol, L-arabitol, arbutin, dulcitol, erythritol, D-fucose, L-fucose, gentiobiose, gluconate, glycerol, inulin, 2-ketogluconate, D-lyxose, methyl
-D-glucoside, methyl
-D-mannoside, methyl
-D-xylose, salicin, sorbose, D-tagatose, D-turanose, xylitol or L-xylose. The cell-wall peptidoglycan contains meso-diaminopimelic acid. The predominant menaquinone is MK-7. The major fatty acids are iso-C15 : 0 and anteiso-C15 : 0. The G+C content of the type strain is 38 mol% (determined by HPLC).
The type strain, TF-12T (=KCCM 41589T=JCM 11545T), was isolated from sea water of a tidal flat of the Yellow Sea in Korea.
| ACKNOWLEDGEMENTS |
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